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<h2>Example applications and input files for OntoFUNC</h2>
<h3>1. Prioritization of candidate genes for genetic diseases</h3>
<p><em>Description:</em> Animal models may provide insights into the
  pathobiology underlying human disease. If a mutation in an animal
  model results in phenotypes <em>similar</em> to a human disease
  phenotype, the animal model may be a good candidate for a disease
  model.
</p>
<p><em>Original
  dataset:</em> <a target="_blank" href="http://compbio.charite.de/hudson/job/hpo/lastStableBuild/">HPO
  annotations of OMIM diseases</a>
  and <a target="_blank" href="ftp://ftp.informatics.jax.org/pub/reports/index.html">MP
  annotated mouse models</a></p>
<p><em>Protocol:</em> The Human Phenotype Ontology and Mammalian
  Phenotype Ontology
  are <a target="_blank" href="http://genomebiology.com/2010/11/1/R2">integrated
  across species</a> based on
  the <a target="_blank" href="http://nar.oxfordjournals.org/content/39/18/e119">PhenomeNET</a>
  system (also
  described <a target="_blank" href="http://rsfs.royalsocietypublishing.org/content/3/2/20120055.full">here</a>).</p>
<p><em>OntoFUNC input
    file:</em> <a href="examples/omim-mgi.txt">omim-mgi.txt</a></p>

<h3>2. Functional similarity of proteins</h2>
<p><em>Description:</em> GO functional similarity between proteins can
  be used as indicator that two proteins interact. Several studies
  applied semantic similarity over GO to predict protein-protein
  interactions and evaluated the results
  (e.g., <a target="_blank" href="http://www.biomedcentral.com/1471-2105/9/472">this study</a>.
</p>
<p><em>Original
  dataset:</em> Gene Ontology Annotations of organisms from
  the <a target="_blank" href="http://www.ebi.ac.uk/GOA">Gene Ontology Annotation</a> project.</p>
<p><em>Protocol:</em> All GO functional annotations
  of <em>C. elegans</em> proteins are obtained from the GOA website
  and used directly for computation of functional similarity.</p>
<p><em>OntoFUNC input
    file:</em> <a href="examples/wbsim.txt">wbsim.txt</a></p>

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